Autoimmune antigens and cancer

ABSTRACT

Autoimmune diseases are thought to be initiated by exposures to foreign antigens that cross-react with endogenous molecules. Analyses of peripheral blood lymphocytes and serum suggested that mutations in autoimmune antigen targets sparked cellular immunity and cross-reactive humoral immune responses. Acquired immunity to autoimmune antigens can help control naturally occurring cancers.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of and claims priority to U.S.application Ser. No. 15/101,174, filed on Jun. 2, 2016, which is a 371application of International Application PCT/US14/68635 filed Dec. 4,2014, which claims priority to U.S. Provisional Application Ser. No.61/911,626, filed on Dec. 4, 2013, the entire contents of which arehereby incorporated by reference.

STATEMENT OF FEDERALLY SPONSORED RESEARCH

This invention was made with government support under CA043460,CA057345, CA062924, AR061439, and AR053503 awarded by the NationalInstitutes of Health. The government has certain rights in theinvention.

TECHNICAL FIELD OF THE INVENTION

This invention is related to the area of immunotherapy. In particular,it relates to the area of immunotherapy and cancer.

BACKGROUND OF THE INVENTION

Systemic sclerosis (scleroderma) is a chronic autoimmune rheumaticdisease associated with widespread obliterative vasculopathy and tissuefibrosis (1, 2). One of the most striking features of this disease isthe temporal clustering of scleroderma and cancer that has been observedin patients with autoantibodies to RPC1 but not in patients withautoantibodies to topoisomerase 1 (TOP1) or centromere protein B (CENPB)(3). A variety of potential mechanisms could explain the occurrence ofcancers in scleroderma patients with autoantibodies to RPC1 (4). Forexample, it is possible that a defective immune system responsible forthe autoimmune disease predisposes to neoplasia, and that this effect ismore prominent in patients with antibodies to RPC1 than in the othersubgroups. Alternatively, it is possible that the cytotoxic, mutagenictherapies used to treat scleroderma patients with more fulminant diseaseleads to cancer in these individuals; patients with RPC1 antibodies tendto have more severe disease than those with other antibodies. Finally,the reverse scenario is possible: cancer might trigger scleroderma inpatients with antibodies to RPC1. In particular, we considered thepossibility that occasional cancers might harbor missense mutations inthe POLR3A gene. If the altered protein encoded by the mutant POLR3Agene were recognized by the patient's immune system, an immune responseagainst the tumor could theoretically be generated. If cross-reactivewith the normal RPC1 protein, this immune response could in turn injureselected tissues thereby inducing scleroderma.

There is a continuing need in the art to develop successful therapiesfor preventing and treating cancers.

SUMMARY OF THE INVENTION

According to one embodiment of the invention a method is provided. Apeptide of 10-40 contiguous amino acid residues of an antigen isadministered to a patient. The antigen is one to which humans can raisean autoimmune response, i.e., a human autoimmune antigen. The peptidecomprises a variant residue relative to the wild-type antigen and bindswith high affinity to an HLA protein of the patient.

According to another embodiment, an isolated peptide of 10-40 contiguousamino acid residues of an antigen is provided. The antigen is one towhich humans can raise an autoimmune response, i.e., a human autoimmuneantigen. The peptide comprises a variant residue relative to thewild-type antigen and binds with high affinity to an human HLA protein.

These and other embodiments which will be apparent to those of skill inthe art upon reading the specification provide the art with new toolsfor combatting cancers in humans.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 Mutant and wild type peptide-specific CD4+ T cells in patientsSCL4 and SCL42. CD154 expression on CD4+ T cells was assayed afterstimulation (18 hr) with patient-specific wild type or mutant RPC1peptides, PAD4 peptide (negative control), or a pool of peptides frominfectious agent antigens (CEFT, positive control). Healthy donorsmatched for one HLA-DR allele were used as controls. Experiments onSCL-4 (A) and SCL-42 (B) were repeated on separate blood draws, threeand two times, respectively, with similar results. Gate frequencies areexpressed as percentage of CD4+ T cells. (C) Frequency ofpeptide-reactive CD4 T cells expressed as fold change over CD154+ CD4 Tcells in the unstimulated negative control.

FIG. 2. Vβ-family usage and CDR3 length in patient SCL-42 PBMCsstimulated with wild type (wt) or mutant peptides. SCL-42 PBMCs(peripheral blood mononuclear cells) were stimulated for 6 days withpatient-specific mutant (gray bars) and corresponding wt (black bars)RPC1 peptides. No appreciable differences in TCR diversity were observedin Vβ8 (A), Vβ17 (B), and Vβ20 (C) TCR families. Skewing of the CDR3length distribution in Vβ7 (D), Vβ12 (E), and Vβ24 (F) TCR families wasobserved and CDR3 lengths that differed by >15% between wt and mutantstimulated PBMCs are indicated (*). CDR3 length is expressed in aminoacids (a.a).

FIG. 3. (Table 1.) Selected clinical and genetic characteristics of thescleroderma patients evaluated in this study

FIG. 4. (Table 2.) Allelic ratios of SNP loci within and closelysurrounding the POLR3A gene.

FIG. 5. (Table 3) Dominant TCR sequences (SEQ ID NO: 97-102,respectively) identified by massively parallel sequencing afterstimulation with wt or mutant peptides

FIG. 6. (FIG. S1.) Immunoprecipitations of wt and mutant RPC proteins bysera from scleroderma cancer patients. ³⁵S-methionine-labeled wt andmutated RPC1 proteins were generated by IVTT (“IVTT Input”). For eachradiolabeled RPC1 protein, the amount used for the input gel samples was1/20 of the amount used for immunoprecipitation. Immunoprecipitates wereelectrophoresed on SDS-polyacrylamide gels and visualized byfluorography. (A) Immunoprecipitations (performed in duplicate) withpatient sera SCL-2, 4 and 42 (“IVTT IP”). The levels of anti-RPC1antibodies in each of the sera (assayed by ELISA) is listed; values >80units denote high levels of these antibodies. (B) Immunoprecipitationswere performed with the indicated scleroderma patient and control sera(right panel, “IVTT IP”).

FIG. 7. (FIG. S2.) Peptide array. Peptides determined to be positivebinders (see Methods) are shown in blue. Only peptides that bound to thesera of at least one patient are displayed, however all 276 peptides(table S4) spanning the entire wt RPC sequence, as well as peptidesspanning the identified POLR3A mutations, were included on the array.

FIG. 8. (FIG. S3.) The effect of HLA-DR blocking antibodies onactivation of CD4+ T cells. PBMCs from patient SCL-42 were stimulatedwith patient-matched mutant and corresponding wild-type RPC1 peptides.The PAD4 peptide and the CEFT pool were used as negative and positivecontrols, respectively. CD4+ T cell responses to RPC1 peptides werereduced by the presence of HLA-DR blocking antibodies (1 ug/ml) but notby an isotype control antibody used at the same concentration.

FIG. 9. (FIG. S4.) Detection of wt and mutant-specific TCRs by qPCR. (A)Patient SCL-4 or SCL -42 PBMCs were cultured with patient-specific wtand mutant peptides for six days prior to cDNA isolation andamplification with Vβ24-based primers specific for the TCRs recognizingthe wt or mutant forms of POLR3A found in patient SCL-42. As indicatedin the lower panel, the relative expression levels of the SCL-42 TCRsfollowing stimulation with the indicated peptides were compared to thoseof GAPDH and displayed as 2^(−ΔCt) (lower panel). (B) Unstimulatedpatient SCL-42 PBMCs were used to generate cDNA which was then amplifiedwith Vβ24-based primers specific for the TCRs recognizing the wt ormutant forms of POLR3A found in patient SCL-42. In the lower panel, thesame cDNA was used to amplify the TCR-β constant region as a positivecontrol.

FIG. 10. (FIG. S5.) Mutant and wild type peptide-specific CD4+ T cellsin patient SCL2. CD154 expression on CD4+ T cells was assayed by flowcytometry after stimulation (18 h) with patient- specific wild type ormutant RPC1 peptides, or a pool of peptides from infectious agentantigens (CEFT, positive control). Gate frequencies are expressed aspercentage of CD4+ T cells.

FIG. 11. (Table S1.) Demographic and clinical characteristics grouped byautoantibody status

FIG. 12. (Table S2.) Primers (forward, reverse, SEQ ID NO: 7-94,respectively) used for loss of heterozygosity analysis.

FIG. 13. (Table S3.) Allelic ratios of SNP loci within and closelysurrounding the TOP1 gene.

FIG. 14. (Table S4.) Synthetic peptides (SEQ ID NO: 151-435,respectively) assessed for antibody reactivity.

FIG. 15. (Table S5.) MHC types of the patients with RPOL3A mutations.

FIG. 16. (Table S6.) Patient-specific MHC class I and class II peptides(wild-type, SEQ ID NO: 103-109, 111-117, 119-124, respectively; mutant,SEQ ID NO: 127-133, 135-141, 143-148, respectively) with highestpredicted binding affinity

DETAILED DESCRIPTION OF THE INVENTION

The inventors have found somatic mutations in autoimmune protein targetsin cancer cells in patients that have both an autoimmune disease and acancer. Patient sera contain T cells specific for the autoimmune proteintargets and antibodies specific for the autoimmune protein targets. Theautoantibodies do not distinguish between mutant and wild-type forms ofthe antigen and do not bind to peptides containing the mutant orwild-type residue. However, some CD4⁺ T cells are reactive with suchmutant peptides. Moreover, the cancer cells containing the somaticmutations appear to comprise only a subset of the cancer cells in thepatient, i.e., they are subclonal. These findings have implications forthe pathogenesis of autoimmune diseases and for the immunologicalcontrol of naturally occurring cancers.

Autoantigens are antigens to which humans can raise an autoimmuneresponse. Autoantigens are a family of proteins that have been found tobe targets of an anti-self immune response associated with diseases.Examples of such diseases are scleroderma, auoimmune rheumatic diseases,such as myositis, vasculitis, and SLE, Sjogren's syndrome, and lupus.Autoantigens known to be involved in such diseases include, but are notlimited to the following:

Lupus

PARP1 P09874.4 GI: 130781 Histone H1 NP_005309.1 GI: 4885371 Histone H2NP_003505.1 GI: 4504249 Histone H3 NP_001005464.1 GI: 53793688 HistoneH4 NP_778224.1 GI: 28173560 SmB Q05856.1 GI: 10720262 SmD P63162.1 GI:52783794 SmG P24715.1 GI: 134126 U1-70k Q62376.2 GI: 83305641 Ro52P19474.1 GI: 133250 Ro60 P10155.2 GI: 52788235 La AAH20818.1 GI:18089160 Ribosomal P2 NP_000995.1 GI: 4506671 Ribosomal P0 NP_444505.1GI: 16933546 Ribosomal P1 P05386.1 GI: 133051 Ki-67 P46013.2 GI:118572663 PCNA P61074.1 GI: 46576879 NPM1 P06748.2 GI: 114762 Defensinbeta Large Gene family . . . Defensin a-4 P12838.2 GI: 399352 Defensina-3 P59666.1 GI: 30316323 Defensin a-1 P59665.1 GI: 30316322 LL37NP_004336.3 GI: 348041314 ASF/SF2 Q07955.2 GI:730773 SR proteinsNP_006702.1 GI: 6857826

Additional in Sjogren's syndrome

IFI-16 Q16666.3 GI: 118572657 AQP4 P55087.2 GI: 2506859 M3R NP_000731.1GI: 4502819 Fodrin alpha Q13813.3 GI: 94730425 Golgin-160 Q08378.2 GI:32470610 GM130 Q08379.3 GI: 294862511 NuMA Q14980.2 GI: 145559510Giantin NP_001243415.1 GI: 374532817 Myositis RBBP7 Q16576.1 GI: 2494891CHD4 Q14839.2 GI: 311033360 RBBP4 (NuRD) Q09028.3 GI: 1172846 MBD3O95983.1 GI: 50400820 SWI/SNF-related O60264.1 GI: 57014128 CHD3Q12873.3 GI: 88911273 HDAC1 Q13547.1 GI: 2498443 PMS1 P54277.1 GI:1709683 PMS2 P54278.2 GI: 317373266 DNA-PK P78527.3 GI: 38258929 RNAhelicase DHX15 O43143.2 GI: 13124667 XRCC4 Q13426.2 GI: 44888352TIF-1g/TRIM 24 O15164.3 GI: 12746552 TIF 1b Q13263.5 GI: 3183179 Ku-70P12956.2 GI: 125729 Ku-86 P13010.3 GI: 125731 NXP2/MORC3 AAI32732.1 GI:124375864 HMGCR P16237.1 GI: 123345 PUF-60 Q9UHX1.1 GI: 74761960 FUBP1Q96AE4.3 GI: 116241370 PM SCL 100k Q01780.2 GI: 8928564 PM SCL 40kNP_001029366.1 GI: 77812672 Histidyl tRNA synthetase P12081.2 GI: 135123Alanyl tRNA synthetase P49588.2 GI: 115502460 Lysyl tRNA synthetaseQ15046.3 GI: 20178333 Threonyl tRNA synthetase P26639.3 GI: 60267755Asparaginyl tRNA synth O43776.1 GI: 3915059 MDA5 Q9BYX4.3 GI: 134047802SRP54 P61011.1 GI: 46577650 SRP 72 O76094.3 GI: 6094347 SRP19 P09132.3GI: 115502457 PALLD Q8WX93.3 GI: 313104206 SAE1 NP_005491.1 GI: 4885585SAE2 NP_005490.1 GI: 4885649

Scleroderma

TOP1 CENP-A P49450.1 GI: 1345726 CENP-B NP_001801.1 GI: 21735415 CENP-CNP_001803.2 GI: 68508961 Fibrillarin CAA39935.1 GI: 31395 RPP30P783461.1 GI: 13124514 RPP40 O75818.3 GI: 238054370 RPB1 P24928.2 GI:281185484 RPB2 P30876.1 GI: 401012 POLR3A (RPC1) O14802.2 GI: 206729892POLR3C (RPC3) Q9BUI4.1 GI: 60393871 POLR3B (RPC2) Q9NW08.2 GI: 29428029POLR3D (RPC4) P05423.2 GI: 29429159 RPC5 Q9NVU0.1 GI: 29428028 RPC6Q9H1D9.1 GI: 20139728 RPC7 O15318.2 GI: 218511818 RPC8 Q9Y535.1 GI:29428071 RPC9 O75575.1 GI: 20532033 RPC10 Q9Y2Y1.2 GI: 116242768 P80coilin P38432.1 GI: 585632 UBF P17480.1 GI: 136652 Nucleolin NP_005372.2GI: 55956788 Centrosomal colon Q86SQ7.1 cancer antigen GI: 74713839CEP250 centrosomal Q9BV73.2 GI: 30580364 PCM1 AAA60120.1 GI: 450277

Vasculitis

Pr3 NP_002768.3 GI: 71361688 MPO NP_000241.1 GI: 4557759 LAMP2NP_054701.1 GI: 7669503

General/RA/other

Vimentin NP_003371.2 GI: 62414289 PAD4 Q9UM07.2 GI: 296439260 IL-1RAP18510.1 GI: 124312

Mutant peptides may display any change in amino acid sequence from thewild type. This can be conveniently determined with regard to thepatient's own normal tissues. Alternatively, wild type found inreference data bases can be used to compare to potential mutantpeptides. A mutant peptide may have one or more single nucleotidesubstitutions, deletions, or insertions. Typically the peptide will havea single nucleotide substitution, deletion, or insertion. In general, itwill have less than four, less than three, or less than two nucleotidesubstitutions, deletions, or insertions. Other than the substitution,deletion, or insertion, the sequence of the peptide will be that of acontiguous stretch of amino acid residues of an autoimmune targetantigen. The contiguous stretch will typically be less than 50, lessthan 40, less than 30, less than 20, less than 18, less than 17, or lessthan 16 amino acid residues. The contiguous stretch will typically be atleast 8, at least 10, at least 12, or at least 13, or at least 14 aminoacid residues. An isolated peptide may be made by any means that ispractical, including by chemical synthesis, enzymatic synthesis, or invivo biosysnthesis. Isolated peptides are not in a cell or in a wholecell lysate. Typically an isolated peptide is a predominant constituentin a composition, i.e., greater than 10, 20, 30, 40, or 50% of theactive ingredients in a composition. A mutant peptide may also be inadmixture with a full length protein of the autoimmune antigen. In suchcase the peptide and the protein may collectively be the predominantconstituents in the composition. A peptide may have other moietiesattached to the contiguous stretch of autoimmune target antigensequence. Such moieties may be, for example, radioactive, fluorescent,enzymatic, or adjuvant moieties.

Cancers which can be treated by use of the mutant peptides include anyto which humans are subject. These include solid and hematologicalcancers, such as breast, lung, ovarian, colorectal, and B cell lymphoma.Other cancers which can be treated include Adenoid Cystic Carcinoma,Adrenal Gland Tumor, Amyloidosis, Anal Cancer, Appendix Cancer,Astrocytoma—Childhood, Ataxia-Telangiectasia, Attenuated FamilialAdenomatous Polyposis, Beckwith-Wiedemann Syndrome, Bile Duct Cancer,Birt-Hogg-Dube Syndrome, Bladder Cancer, Bone Cancer, Brain StemGlioma—Childhood, Brain Tumor, Breast Cancer, BreastCancer—Inflammatory, Breast Cancer—Male, Breast Cancer—Metaplastic,Carcinoid Tumor, Carney Complex, Central Nervous System—Childhood,Cervical Cancer, Childhood Cancer, Colorectal Cancer, Cowden Syndrome,Craniopharyngioma—Childhood, Desmoplastic InfantileGanglioglioma—Childhood Tumor, Endocrine Tumor, Ependymoma—Childhood,Esophageal Cancer, Ewing Family of Tumors—Childhood, Eye Cancer, EyelidCancer, Fallopian Tube Cancer, Familial Adenomatous Polyposis, FamilialMalignant Melanoma, Familial Non-VHL Clear Cell Renal Cell Carcinoma,Gallbladder Cancer, Gardner Syndrome, Gastrointestinal StromalTumor—GIST, Germ Cell Tumor—Childhood, Gestational Trophoblastic Tumor,Head and Neck Cancer, Hereditary Breast and Ovarian Cancer, HereditaryDiffuse Gastric Cancer, Hereditary Leiomyomatosis and Renal Cell Cancer,Hereditary Mixed Polyposis Syndrome, Hereditary Pancreatitis, HereditaryPapillary Renal Cell Carcinoma, HIV and AIDS-Related Cancer, Islet CellTumor, Juvenile Polyposis Syndrome, Kidney Cancer, Lacrimal Gland Tumor,Laryngeal and Hypopharyngeal Cancer, Leukemia—AcuteLymphoblastic—ALL—Childhood, Leukemia—Acute Lymphocytic—ALL,Leukemia—Acute Myeloid—AML, Leukemia—Acute Myeloid—AML—Childhood,Leukemia—B-cell Prolymphocytic Leukemia and Hairy Cell Leukemia,Leukemia—Chronic Lymphocytic—CLL, Leukemia—Chronic Myeloid—CML,Leukemia—Chronic T-Cell Lymphocytic, Leukemia—Eosinophilic, Li-FraumeniSyndrome, Liver Cancer, Lung Cancer, Lymphoma—Hodgkin,Lymphoma—Hodgkin—Childhood, Lymphoma—Non-Hodgkin,Lymphoma—Non-Hodgkin—Childhood, Lynch Syndrome, Mastocytosis,Medulloblastoma—Childhood, Melanoma, Meningioma, Mesothelioma,Muir-Torre Syndrome, Multiple Endocrine Neoplasia Type 1, MultipleEndocrine Neoplasia Type 2, Multiple Myeloma, MyelodysplasticSyndromes—MDS, MYH-Associated Polyposis, Nasal Cavity and ParanasalSinus Cancer, Nasopharyngeal Cancer, Neuroblastoma—Childhood,Neuroendocrine Tumor, Neurofibromatosis Type 1, Neurofibromatosis Type2, Nevoid Basal Cell Carcinoma Syndrome, Oral and Oropharyngeal Cancer,Osteosarcoma—Childhood, Ovarian Cancer, Pancreatic Cancer, ParathyroidCancer, Penile Cancer, Peutz-Jeghers Syndrome, Pituitary Gland Tumor,Pleuropulmonary Blastoma—Childhood, Prostate Cancer,Retinoblastoma—Childhood, Rhabdomyosarcoma—Childhood, Salivary GlandCancer, Sarcoma, Sarcoma—Alveolar Soft Part and Cardiac, Sarcoma—Kaposi,Skin Cancer (Non-Melanoma), Small Bowel Cancer, Stomach Cancer,Testicular Cancer, Thymoma, Thyroid Cancer, Tuberous Sclerosis Syndrome,Turcot Syndrome, Unknown Primary, Uterine Cancer, Vaginal Cancer, VonHippel-Lindau Syndrome, Vulvar Cancer, Waldenstrom's Macroglobulinemia,Werner Syndrome, Wilms Tumor—Childhood, and Xeroderma Pigmentosum.

Binding to human HLA proteins and measurement of the binding can beperformed according to any methods known in the art. One method whichcan be employed uses in silico tools such as Immune Epitope Database(IEDB) analysis resource Consensus tools (7-9). High affinity binding isassessed when the IC₅₀ is <50 nM. Moderately high affinity binding isassessed when the IC₅₀ is <125 nM. Extremely high affinity binding isassessed when the IC₅₀ is <10 nM. Ascertainment of the type of HLAproteins present in a human can be performed using any methods known inthe art. Exemplary methods include serotyping, cellular typing, genesequencing, and phenotyping.

A subset of patients with scleroderma and other autoimmune rheumaticdiseases manifest cancer around the time of autoimmune diseasediagnosis, suggesting that the two processes might be linkedmechanistically (3), (4), (17). In scleroderma, this temporal clusteringof scleroderma and cancer appears limited to the subgroup of patientswith antibodies to RPC1 (3). In the current work, we demonstrated thatthe POLR3A locus is genetically altered (by somatic mutation or LOH) insix of eight cancers of patients with antibodies to RPC1, but not incancers from scleroderma patients with other autoantibody specificities.Moreover, T cells reactive with the mutant forms of RPC1 could beidentified in the peripheral blood of two of the three patients tested.These T cells did not simply cross-react with the wild-type form of thepeptides, because T cells from subject SCL-4 were not stimulated by thewild type form, and the sequence of the TCRs conferring responsivenessto the wild type and mutant peptides in SCL-42 were largely unrelated.

These genetic and immunologic findings suggest mutation in POLR3A as theinitiator of the immune response to RPC1 in an important subset ofscleroderma patients. The only tenable alternative to this conclusion isthat the onset of scleroderma and the cancer genomes of these patientswere unrelated and that the missense mutations and T cell responsesdirected against the same mutations were coincidental. We believe thisalternative is unlikely given the rarity of POLR3A mutations in cancerin general (0.7%, p<10⁻²⁰, cosmic database, (18), and the absence ofalterations at this locus in scleroderma patients without RPC antibodies(p<0.01). Additionally, in patient SCL-42, there were multiple differentnucleotide sequences encoding TCRs with the identical amino acidsequence in T cells stimulated by the mutant peptide (Table 3). Thisprovides strong support for the conclusion that the mutant POLR3A geneproduct acted as an immunogen initiating the anti-RPC1 immune responsein vivo.

Antibodies from all patients with POLR3A mutations recognized wild typeand mutant versions of RPC1 similarly, and no antibodies directedspecifically against the wild type or mutant peptides could bedemonstrated. This suggests that the humoral response does not directlytarget the area of the mutation or discriminate between mutant and wildtype versions of RPC1. The inability of autoantibodies to discriminatebetween the mutant and wt forms of the antigen is consistent withprevious studies showing that a crossreactive humoral response istypical when a novel form of an antigen initially stimulates T cellsthat specifically recognize the modified antigen (19, 20). The antibodycross-reactivity might contribute to B cell-mediated diversification ofautoimmunity, spreading T cell responses to the wild type autoantigen(21, 22).

Our data therefore suggest that the “foreign” antigen triggering theautoimmune response in scleroderma patients is actually a tumor antigen.This complements previous observations indicating cancers can elicitimmune responses. It is known that some cases of paraneoplastic syndromeare caused by autoimmunity to proteins expressed in tumors (23); theseresponses are directed exclusively to the normal protein and there is noevidence that the gene(s) are mutated in the tumors. Conversely, it hasbeen shown that mutant genes in human tumors can elicit an immuneresponse against the mutant gene product (24-26); these immune responseshave not been shown to elicit a cross-reactive response to the normalgene product that could result in autoimmunity. Finally, it has beenshown that an in vitro-generated protein containing multiple (but notsingle) mutations, when injected into mice, can elicit a broad,cross-reactive immune response against the normal protein that resultsin autoimmunity (27). In these mice, tumor cells expressing only the wtprotein can also be targeted by the subsequent immune response. Ourresults show that an analogous situation appears to occur in humans whena single, strongly immunogenic epitope is created by somatic mutation ina patient with an appropriate MHC type. However, the generation of anautoreactive immune response alone may not be sufficient to generate theself-sustaining tissue injury seen in scleroderma, and additionalfactors (genetic, environmental, or target tissue-specific) may berequired (28).

Our cohort included cancer patients without anti-RPC1 antibodies (Table1). While the interval between scleroderma and cancer onset for patientsin these patients was long (median of 14.2 years), there were two,patients (SCL-8 and SCL-32) who had relatively short intervals. We didnot identify genetic alterations of TOPO1 or CENPB in these twopatients. Whether their cancers were adventitious, related to therapy,or due to mutations in genes encoding homologs of TOPO1 or CENPB orproteins that interact with them is unknown but are intriguinghypotheses for future study. Similar factors could also explain theabsence of genetic alterations of POLR3A in two of the eight patientswith antibodies to RPC1.

The relatively low fraction of neoplastic cells with genetic alterationsin the cancers from some of these patients (Tables 1 and 2) suggeststhat immunoediting of the cancer had occurred, with cells containingthese mutations selected against during tumor growth (29). The emergenceof cancer in RPC1-positive scleroderma patients may thereby representescape of the tumor from immune pressure. We speculate that cancersharboring POLR3A mutations had stimulated scleroderma in most patientswith the RPC1 form of the disease. However, in the majority of thesepatients, the immune response had eradicated the cancer by the timescleroderma developed. Patients with a short cancer-autoimmune diseaseinterval have also been described for other autoimmune rheumatic diseasephenotypes (e.g. myositis, vasculitis, SLE) and similar mechanisms maybe operative in these diseases (17, 30, 31). Given the ubiquitouspresence of somatic mutations in solid tumors (32), these new data addcredence to the idea that immunoediting could play a major role inlimiting the incidence of human cancer—an old hypothesis (33, 34) thathas recently garnered more attention (35-37). The data also suggest thatthis family of autoantigens might be used to generate biologicallyeffective anti-tumor immunity.

The above disclosure generally describes the present invention. Allreferences disclosed herein are expressly incorporated by reference. Amore complete understanding can be obtained by reference to thefollowing specific examples which are provided herein for purposes ofillustration only, and are not intended to limit the scope of theinvention.

EXAMPLE 1 Genetic Analysis

We began by searching for missense mutations in the POLR3A gene intumors from scleroderma patients. We were able to collect tumor andnormal tissue samples from eight scleroderma patients who hadautoantibodies to RPC1. We also evaluated eight scleroderma patients whohad autoantibodies to TOP1 or to CENPB and developed cancers (Table 1).Five of the patients with antibodies to RPC1 developed cancer prior toscleroderma (median of 0.4 years before scleroderma onset), while theremaining 3 developed cancer 0.3-2.5 years after the onset ofscleroderma (Table 1). In contrast, patients with autoantibodies toCENPB or TOP1 who developed cancers only did so a median of 14.2 yearsafter the onset of their scleroderma (Table 1). The characteristics ofthe 16 scleroderma patients, including tumor type, age of diagnosis ofcancer, cancer-scleroderma interval, and autoantibody status, are listedin Table 1; additional clinical information is provided in table S1 and(5).

Formalin-fixed, paraffin-embedded tumors from each of the 16 patientswere microdissected to enrich for neoplastic cell content, and DNA waspurified, blunt-ended, and ligated to adapters suitable for librarypreparation (5). Libraries from peripheral blood cells of each patientwere similarly prepared. Following amplification of the 32 libraries (16tumor, 16 matched normal), the PCR products were captured usingPCR-generated fragments containing all coding sequences of the POLR3A,TOP1, and CENPB genes (5). The captured fragments were evaluated bysequencing on an Illumina instrument, achieving an average coverage of516 reads per base of the 53 coding-exons of the three genes (range 95-to 2011-fold).

This sequence revealed three somatic, missense variants in POLR3A andnone in TOP1 or CENPB (Table 1). All three variants were in the patientswith autoantibodies to RPC1. The three somatic mutations were eachvalidated by massively parallel sequencing of PCR products generatedfrom the regions surrounding the mutations (5). Of note, both thecapture approach and the direct-PCR sequencing approach showed that oneof the three somatic mutations was decidedly subclonal, that is, waspresent in only a subset of the neoplastic cells: the fraction of mutantalleles in the lung cancer from patient SCL-2 was only 4.3%, far lessthan the estimated fraction of neoplastic cells in the microdissectedsample used for DNA purification (Table 1) (5).

In light of the subclonal nature of one of these mutations, weconsidered the possibility that cells containing these mutations wereselected against during tumor growth, perhaps even disappearing as aresult of an immune response. The most frequent way to lose a mutantallele in human cancers is through a gross chromosomal event thatresults in loss of the entire gene and the surrounding chromosomalregion (loss of heterozygosity, LOH) (6). To search for such losses, wedesigned 19 primer pairs that could each amplify a small fragmentcontaining at least one common single nucleotide polymorphism (SNP)within or surrounding the POLR3A gene (table S2). These primer pairswere used in a multiplexed protocol to evaluate all 16 tumors (5). Fiveof the eight tumors from scleroderma patients with autoantibodies toRPC1 exhibited LOH (Table 2). These five tumors included three that didnot contain a detectable somatic mutation of POLR3A (Table 1). Thefraction of neoplastic cells that had undergone LOH could be estimatedfrom the allelic ratios of the SNP data, and in four of the five cases,was subclonal (Table 2). Importantly, none of the tumors from patientswith antibodies to TOP1 or CENPB exhibited LOH of the region containingPOLR3A (Table 2). As an additional control, we evaluated 21 SNPs withinor surrounding the TOP1 locus on chromosome 20 (table S2) and found thatnone of the 16 tumors from scleroderma patients, regardless ofautoantibody status, had undergone LOH of this region (table S3).

In summary, six of eight tumors from scleroderma patients withautoantibodies to RPC1 harbored genetic alterations affecting the POLR3Alocus compared to zero of eight tumors from scleroderma patients withoutanti-RPC1 antibodies (p<0.01, Fisher Exact Probability Test,two-tailed).

EXAMPLE 2 Immunological Analysis

We began the immunological analysis of these patients by addressingwhether RPC1 autoantibodies recognized the mutated protein differentlyfrom the wild type (wt) form of the protein. Each of the three abnormalforms of the protein found in scleroderma patients was synthesized by invitro transcription-translation (IVTT) (5). Wild type andpatient-matched mutant RPC1 were then subjected to immunoprecipitationanalysis with sera from patients or from normal individuals (controlsera). In each case, mutant and wt proteins were precipitated similarlyby patient serum, but not precipitated by control sera (FIG. S1),demonstrating that the autoantibodies do not discriminate between wildtype and mutant versions of the antigen.

We next constructed a custom peptide microarray to comprehensivelyidentify linear antigenic regions of the RPC1 protein. We synthesized276 overlapping peptides of 15 amino acids in length, each offset byfive amino acids from the previous peptide and covering the entirelength of RPC1 (table S4). Peptides that contained each of the threesomatic mutations described above were also synthesized (three peptidesfor each mutant; table S4). These peptides were printed on microarraysand used to assess serum from the three patients with antibodies to RPC1(SCL-02, SCL-04, and SCL-42) whose cancers harbored POLR3A mutations,and four control patients (SCL-200, SCL-201, SCL-202, SCL-203) who hadscleroderma and antibodies to RPC1 but who did not have cancers. Each ofthe seven serum samples displayed reactivity with at least two of thepeptides on the array (fig. S2). Notably, there was no reactivity to themutant peptides or their wild type counterparts (i.e., wt amino acids inplace of mutant amino acids) in sera from the patients whose cancersharbored these mutations (or in the other patients).

Having shown that there was no demonstrable humoral immune responsespecific to the mutant RPC1 proteins, we sought to determine if therewas a cellular immune response directed against the mutants. We firstperformed high-resolution class I and II HLA typing on the threescleroderma patients in whom somatically mutated POLR3A genes wereidentified (table S5). IEDB analysis resource Consensus tools (7-9) werethen used to determine whether peptides containing the specificmutations in individual patients were likely to bind with high affinityto that patient's HLA alleles. In patient SCL-42, both wild type andmutant epitopes were predicted to bind with high affinity to bothalleles of the patient's class II DR HLA (table S6). This wasparticularly dramatic for HLA-DR*0701, where the predicted ICso was <1nM for both the mutant (FHVGYFRAVIGTLQMI; SEQ ID NO: 95) and wild typepeptides (FHVGYFRAVIGILQMI; SEQ ID NO: 96; table S6). High affinitybinding of the wild type and mutant peptides to this patient's other DRallele (HLA-DR*1001) was also predicted (table S6). In patient SCL-4,the mutant peptide was predicted to bind to this patient's HLA-DR*0101allele with an affinity of 4 nM, 18-fold higher than the affinity of thewt peptide (table S6). The wild type peptide in this region was alsopredicted to bind, albeit less strongly, to this patient's second allele(26 nM to HLA-DR*1101). Neither wild type nor mutant peptides werepredicted to bind with high affinity to the class II molecules ofpatient SCL-2 (table S6). The algorithms also predicted binding ofpatient-matched wild type and mutant peptides to a single HLA class Iallele in each patient, though the binding affinities were only moderate(27 to 78 nM, table S6).

CD4 cells are known to recognize peptides presented by MHC class IIalleles and play central roles in both tumor immunity and autoimmunity(10, 11). In light of this knowledge and our finding that the predictedaffinities for class II peptides were much higher than for class Ipeptides, we searched for CD4 T cells recognizing the predicted peptidesin PBMCs from patients whose tumors contained POLR3A mutations. CD154expression at 18 hours after peptide stimulation was used to identifypeptide-activated CD4+ T cells (12, 13). In patient SCL-4, CD4 T cellactivation was observed in response to the patient-matched mutantpeptide but not to the wt peptide (FIG. 1A, C). Moreover, no CD4 T cellresponses to these peptides were observed in T cells from a healthycontrol matched with SCL-4 at HLA-DR*1101 (FIG. 1A). Thus, theexperimental data confirmed the in silico predictions.

The experimental data also confirmed the predicted reactivity of T cellsfrom patient SCL-42, with a 2-fold increase in the number of CD4+CD154+T cells in response to both the wt and mutant SCL-42 peptides overcontrol conditions. The frequency of responding cells was about a loglower in SCL-42 compared to SCL-4, with ˜1:5,000 CD4 T cells responding(FIG. 1B, C). The CD4 T cell responses to wt and mutant SCL-42 peptideswere abolished by treatment with anti-HLA-DR antibodies but not by anisotype control (FIG. S3). As in patient SCL-4, no response to RPC1peptides was observed in T cells from a healthy control matched withSCL-42 at HLA-DR*0701 (FIG. 1B). As predicted by the in silico bindingalgorithms (table S6), patient SCL-2 did not respond to either wild typeor mutant peptides, but did express CD154 in response to the positivecontrol stimulus, demonstrating that her cells were immune competent(FIG. S5).

These data document the existence of CD4 T cells reactive with peptidescontaining the RPC1 mutations in two of the three patients studied. Thereactivity was patient, peptide, and HLA-type specific. The frequenciesof mutant peptide-reactive CD4 T cells observed in these sclerodermapatients (˜1:600 to ˜1:5000, FIG. 1) were in the range observed forantigen-specific CD4+ T cells observed in other autoimmune processes(14). SCL-4 responded only to the mutant peptide, while patient SCL-42responded to the mutant as well as to the wt peptides (FIG. 1C).

It was possible that the CD4 T cells that were activated in response tothe mutant peptide in SCL-42 were the same as those responding to the wtpeptide. To evaluate this issue, we performed TCR spectratyping of Tcells stimulated by either wt or mutant peptides. Out of the 22 Vβfamilies analyzed, 12 displayed a similar distribution of their CDR3lengths in response to wt and mutant peptides including Vβ8, Vβ17, andVβ20 (FIG. 2A-C). In contrast, significant differences in thedistribution of CDR3 lengths were observed for several other Vβs (Vβ3,Vβ5, Vβ7, Vβ12, Vβ16 and Vβ24) (FIG. 2D-F). For some Vβs, marked skewingin CDR3 lengths was observed, with >25% of TCRs from cells- treated witheither the mutant or the wt form of the peptide represented by a singleCDR3 length. These data suggested that the T cells responding to themutant peptides were not, in general, those responding to the wtpeptides.

To characterize the TCRs in more detail, we determined the sequence ofthe CDR3 regions in the Vβ7, Vβ12 and Vβ24 PCR products (5). Twostriking findings were revealed by massively parallel sequencing ofthese regions. First, the sequences of the dominant TCRs generated fromTcells stimulated with the wt peptide were completely distinct fromthose stimulated by the mutant peptide (Table 3). In 5 of 6 dominantTCR's identified by sequencing, the wt- and mutant-specific CDR3sequences were precisely the lengths predicted by the spectratypeanalysis (Table 3). The sequencing results therefore strongly supportedthe conclusion from spectratyping that the mutant and wt peptides hadstimulated many distinct T cell clones. Second, there was a high degreeof redundancy among the amino acid sequences—but not the nucleotidesequences—of the TCRs identified in this experiment. For example, weidentified 17 different nucleotide sequences (represented by 2066clusters on the sequencing instrument) that encoded the identical CDR3amino acid sequence in T cells stimulated by the mutant peptide (Table3). As T cells, unlike B-cells, do not undergo continued evolution oncea successful VDJ rearrangement has occurred (15, 16), these datadocument the existence of multiple, independent T cell clonesresponding, and presumably binding, to the same mutant peptide.

Finally, we developed CDR3-specific Taqman assays to verify thatdistinct populations of wt and mutant-specific T cells were present inthe peripheral blood of SCL-42 prior to the short-term cultures used inthe experiments described above. The Vβ24 TCRs were chosen for thisexperiment because their CDR3 sequences were the most abundant in thesequencing analysis and were each encoded by multiple distinctnucleotide sequences (Table 3). The TCRs expected to bind the mutant andwild type peptides were detected in uncultured SCL-42 PBMCs (FIG. S4).Neither TCR was detectable in the PMBCs of patient SCL-4, used as acontrol.

EXAMPLE 3

Materials and Methods

Clinical Methods

Consenting scleroderma patients with confirmed cancer diagnoses wererecruited from the Johns Hopkins Scleroderma Center. Sclerodermapatients met the American College of Rheumatology criteria forscleroderma (38). Existing cancer pathology specimens were obtained fromprior surgical procedures performed as part of routine clinical care.The closest serum sample to cancer diagnosis was studied in allpatients, and DNA and PBMC samples were obtained in consentingparticipants. The Johns Hopkins Institutional Review Board approved theacquisition of clinical data and all biological samples for this study.

Demographic and clinical data were abstracted from the Johns HopkinsScleroderma Center database and careful medical record review. Cancerdiagnosis dates and histology were determined by review of the initialdiagnostic pathology report. The clinical onset of scleroderma wasdefined by the first scleroderma symptom, either Raynaud's ornon-Raynaud's. The interval between scleroderma onset and cancerdiagnosis was calculated for each subject (cancer date—scleroderma onsetdate). The scleroderma cutaneous subtype and modified Rodnan skin scorewere defined by established criteria (39, 40). All sera were tested forautoantibodies against RPC1, TOP1, and CENPB as previously described(3). Demographic and clinical data were compared across autoantibodygroups, and differences in continuous and dichotomous/categoricalvariables were assessed by the Kruskal-Wallis and Fisher's exact tests,respectively.

The clinical features and cancer types of the 16 patients evaluated inthis study are listed in Table 1. Eight patients were positive foranti-RPC1 antibodies, five for anti-TOP1 antibodies and three foranti-CENPB antibodies. Enhanced nucleolar staining with the anti-RPC1antibodies (3) was observed in the tumors of all eight patients. Nosubject was positive for more than one autoantibody. Clinical phenotypiccharacteristics were representative of those expected in eachautoantibody group (e.g. severe diffuse disease in RPC1-positivepatients), and patients with RPC1 autoantibodies had a shorter intervalbetween scleroderma onset and cancer diagnosis (median of −0.1 years vs.13.4 years for patients with TOP1 autoantibodies and 34.0 years forpatients with CENPB autoantibodies; p=0.05). Seven of the 16 patientshad a short interval (+/−2 years) between scleroderma onset and cancerdiagnosis, and 6 of these 7 patients (85.7%) were positive for anti-RNApolymerase III antibodies.

Preparation of Illumina Genomic DNA Libraries

Genomic DNA libraries were prepared following Illumina's (Illumina, SanDiego, Calif.) suggested protocol with the following modifications. (1)50 to 75 microliters (μ1) of genomic DNA from tumor or normal cells in atotal volume of 100 μl. TE was fragmented in a Covaris sonicator(Covaris, Woburn, Mass.) to a size of 100 to 500 bp. DNA was purifiedwith a Nucleospin Extract II kit (Cat #740609, Macherey-Nagel, Germany)and eluted in 50 μl of elution buffer included in the kit. (2) 45 μl ofpurified, fragmented DNA was mixed with 40 μl of H₂O, 10 μl End repairreaction buffer and 5 μl of End Repair enzyme. All reagents used forthis step and those described below were from New England Biolabs (NEBcat # E6040, Ipswich, Mass.) unless otherwise specified. The 100 μlend-repair mixture was incubated at 20° C. for 30 min, purified by a PCRpurification kit (Cat #28104, Qiagen) and eluted with 42 μl of elutionbuffer (EB). (3) To A-tail, all 42 μl of end-repaired DNA was mixed with5 μl of 10× dA-Tailing Reaction buffer and 3 μl of Klenow Fragment (3′to 5′ exo-). The 50 μl mixture was incubated at 37° C. for 30 min beforeDNA was purified with a MinElute PCR purification kit (Cat #28004,Qiagen). Purified DNA was eluted with 27 μl of 70° C. EB. (4) Foradaptor ligation, 25 μl of A-tailed DNA was mixed with 10 μl ofPE-adaptor (Illumina), 10 μl of 5×Ligation buffer and 5 μl of Quick T4Ligase. The ligation mixture was incubated at room temperature (RT) or20° C. for 15 min. (5) To purify adaptor-ligated DNA, 50 μl of ligationmixture from step (4) was mixed with 200 μl of NT buffer from NucleoSpinExtract II kit (cat #636972, Clontech, Mountain View, Calif.) and loadedinto a NucleoSpin column. The column was centrifuged at 14000 g in adesktop centrifuge for 1 min, washed once with 600 μl of wash buffer(NT3 from Clontech), and centrifuged again for 2 min to dry completely.DNA was eluted in 50 μl elution buffer included in the kit. (6) Toobtain an amplified library, ten or twenty PCRs of 50 μl each weresetup, each including 30 μl of H₂O, 2.5 μl dimethyl sulfoxide (DMSO), 10μl of 5×Phusion HF buffer, 1.0 μl of a dNTP mix containing 10 mM of eachdNTP, 0.5 μl of Illumina PE primer #1, 0.5 μl of Illumina PE primer #2,0.5 μl of Hot Start Phusion polymerase, and 2.5 or 5 μl of the DNA fromstep (5). The PCR program used was: 98° C. 1 minute; 10 to 16 cycles of98° C. for 20 seconds, 65° C. for 30 seconds, 72° C. for 30 seconds; and72° C. for 5 min. To purify the PCR product, 250 μl PCR mixture (fromthe ten PCR reactions) was mixed with 500 μl NT buffer from a NucleoSpinExtract II kit and purified as described in step (5). Library DNA waseluted with 70° C. elution buffer and the DNA concentration wasestimated by absorption at 260 nm.

Target DNA Enrichment

The targeted regions included all 53 exons of CENPB, POLR3A, TOP1.Capture probes were designed (41) to capture both the plus and the minusstrand of the DNA and had a 33-base overlap and were custom-synthesizedby Agilent Technologies en masse on a solid phase and used for capture,essentially as described (42). Approximately 3 μg of library DNA wasused per capture. After washing, the captured libraries wereethanol-precipitated and redissolved in 20 μl of Tris-EDTA (TE) buffer.The DNA was then amplified in a PCR mix containing 51 μl of distilledwater (dH₂O), 20 μl of 5× Phusion buffer, 5 μl of dimethyl sulfoxide(DMSO), 2 μl of 10 mM dNTPs, 50 pmol of Illumina forward and reverseprimers, and 1 μl of HotStart Phusion enzyme (New England Biolabs) withthe following cycling program: 98° C. for 30 s; 15 cycles of 98° C. for25 s, 65° C. for 30 s, 72° C. for 30 s; and 72° C. for 5 min. Theamplified PCR product was purified with a NucleoSpin column (MachereyNagel Inc.) according to the manufacturer's suggested protocol, exceptthat the NT buffer was not diluted and the DNA bound to the column waseluted in 45 μl of elution buffer. The captured libraries werequantified using an Agilent BioAnalyzer.

Somatic Mutation Identification and LOH Analysis

Captured DNA libraries were sequenced with the Illumina GAIIx GenomeAnalyzer. Sequencing reads were analyzed and aligned to human genomehg18 with the Eland algorithm in CASAVA 1.6 software (Illumina). Amismatched base was identified as a mutation only when (i) it wasidentified by ten or more distinct pairs; (ii) the number of distincttags containing a particular mismatched base was at least 2.5% of thetotal distinct tags; and (iii) it was not present in >0.5% of the tagsin the matched normal sample. Mutations were confirmed by amplificationof the relevant region with a single primer pair and evaluated asdescribed in (43). LOH analysis was performed in a similar way, usingthe primer pairs described in table S3. A patient was considered“informative” for the SNP if DNA from the normal tissue of that patientwas heterozygous for the SNP. A tumor was determined to have undergoneLOH if >75% of the informative primer pairs in that patient had anallelic ratio less than the mean minus 2 standard deviations of thosemeasured in control individuals without scleroderma. Note that thisanalysis can only assess allelic imbalance, i.e., a gain in one alleleor a loss in the other allele, though it is often (including in thecurrent study) interpreted as LOH, i.e., loss of an allele.

Peptide Microarray

All experiments with the peptide microarray were performed at ProImmuneInc. (Oxford, UK). Peptides were synthesized as 15-mers with 10overlapping amino acids from the previous peptide, spanning the entireRPC1 protein. Peptides were printed on glass slides with multiple arraysper slide separated with gaskets, allowing for multiple donor sera to betested per slide. Donor serum was diluted 1:100, 1:500 and 1:1000 andincubated on the array. A fluorescent anti-Human IgG antibody was usedas a secondary antibody, results were detected using a CCD camera andanalysis was done using MS Excel. Peptides were determined to bepotential binders if the normalized average signal intensity was greaterthan 4× the respective background negative control. Binding wasconsidered positive if the signal intensity was 4× background for allthree serum dilutions.

Autoantibody Analysis

RPC1 antibodies were assayed by ELISA using a commercially available kit(Inova Diagnostics). CENP and TOP1 autoanitibody assays were performedas described in (3). To define whether patient antibodies recognizedpatient-specific mutated forms of RPC1, full-length wild type humanPOLR3A cDNA was purchased from Origene, and site-directed mutagenesiswas performed to generate the three different RPC1 mutants, each with asingle point mutation: E1072Q, K1365N and I104T, corresponding to thetumor mutations detected in patients SCL-2, SCL-4 and SCL-42,respectively. All were sequence verified before use.³⁵S-methionine-labeled products were generated from the wild type andmutant DNAs by IVTT reactions (Promega kit). Prior to use inimmunoprecipitations, the radiolabeled proteins were electrophoresed onSDS-PAGE gels and visualized by fluorography. The radiolabeled signalgenerated by each of these products was similar (1 μl of E1072Qequivalent to: 1.1, 1.2 and 1.7 μl of I104T, wt and K1365N,respectively). Equivalent radioactive amounts ³⁵S-methionine-labeled wtand mutated RPC1 proteins were used in immunoprecipitations performed asdescribed in (44) with sera from three cancer scleroderma patients. Oneμl of each serum was used to immunoprecipitate the wild-type form ofRPCJ as well as the specific RPCJ mutation found in the tumor from thatpatient.

Cell Culture, Stimulation and Flow Cytometry

PBMCs were freshly isolated from whole blood by density-gradientcentrifugation (Ficoll-Paque Plus, GE Healthcare), and were used fresh(SCL-42) or frozen (SCL4 and SCL2). For each patient, PBMCs from a donorexpressing one matching HLA-DRB1 allele was selected and used as acontrol. Cells were resuspended to a concentration of 1.5×10⁶ cells/150μl in RPMI medium supplemented with serum, 2mM L-glutamine, 100 U/mlpenicillin, and 100 μg/ml streptomycin, and were plated onto 96-wellflat bottom plates. 1 μg/ml anti-human CD40 blocking antibody (G28.5,Biolegend) was added, and after 30 minutes, cells were stimulated for 18hours as indicated: 4 μg/ml wild-type or mutant patient-matched RPC1peptide, 4 μg/ml of peptidyl arginine deiminase 4 (PAD4) peptide as anegative control, or 4 μg/ml of a pool of class-II peptides frominfectious agents antigens (CEFT) (Axxora) as a positive control.Peptide storage buffer was used for the unstimulated control. HLArestriction was assessed by stimulating cells in the presence of 1 μg/mlanti-HLA-DR blocking antibody (L243, Biolegend) or 1 μg/ml IgG-2a κisotype control (MOPC-173, Biolegend).

Cells were washed with PBS after stimulation, stained with live/deadfixable blue dead cell stain (Molecular Probes), and then stained withBV510-conjugated CD3 antibody (OKT3, BioLegend), Pacific Blue-conjugatedanti-CD4 antibody (RPA-T4, BD Pharmingen), APC-H7-conjugated anti-CD8(SK1, BD), and PE-conjugated anti-CD154 antibody (TRAP1, BD Pharmingen).FACS analysis was performed on FACSAria flow cytometer-cell-sorter usingFACSDiva (Becton Dickinson) and FlowJo software (Tree Star Inc. Ashland,Oreg., USA).

TCR Spectratyping

The diversity of CDR3 regions for 22 TCR Vβ regions was assessed usingthe TCRExpress Quantitative Analysis Kit (Biomed Immunotech, TampaFla.). Briefly, RNA was isolated from SCL-42 PBMCs after culture for 6days with wt or mutant peptides (Invitrogen, Carlsbad Calif.), and cDNAwas generated using random hexamers (Invitrogen) and You Prime FirstStrand Beads (GE, Buckinghamshire UK) following the manufacturersprotocols. CDR3 regions were amplified from cDNA using two rounds of PCRwith Vβ-family specific PCR primers as per the manufacturer'sinstructions. Fragment length analysis was performed by the JohnsHopkins DNA analysis facility. The distribution of CDR3 lengths for eachVβ-family was determined and expressed as “proportion of TCR”. Peakswere considered to be antigen-driven when the observed proportion of agiven fragment size differed by more than 10% between wt andmutant-stimulated cells.

TCR Sequencing

TCR libraries were prepared for sequencing using a Truseq samplepreparation kit following the manufacturer's suggestions with thefollowing modifications. Input DNA was prepared from the PCR productsobtained from spectratyping analysis. Product from wells using primersspecific to the CDR3 regions of Vβ3, Vβ5, Vβ7, Vβ12, Vβ16 and Vβ24 werepurified using a Qiagen PCR purification kit. DNA was eluted in 30 ul of65° C. elution buffer. After A-tailing and igation to adaptors, thelibrary was amplified in six reactions with a PCR mix containing 10 ulH20, 1.5 μl DMSO, 6 ul 5× Phusion buffer, 6 ul dNTPs, 3 ul each ofForward and Reverse Primers, 3 ul Phusion polymerase (2 U/ul) and 2 ulligation reactions, and cycled using the following program, 98° C. for30 s; 14 cycles of 98° C. for 10 s, 65° C. for 30 s, 72° C. for 30 s;and 72° C. for 5 min. The resulting product was purified using Ampurebeads, quantified with an Agilent Bioanalyzer, and sequenced using anIllumina instrument.

qPCR Detection of Specific TCRs

Custom Taqman assays for specific TCRs were developed using Primerexpress v2.0 software and synthesized by Applied Biosystems. Fordetection of the Vβ24 Jβ1.1 wt TCR, a FAM-labeled probe(ACTGAAGCTTTCTTTGGAC; SEQ ID NO: 1), forward primer(GCACCGGGACAGTGATGAA; SEQ ID NO: 2), and reverse primer(GGTCCTCTACAACTGTGAGTTTGGT; SEQ ID NO: 3) were synthesized. Fordetection of the Vβ24 Jβ1.5 mutant TCR, a FAM-labeled probe(ACAGTAAATCAGCCCCAGC; SEQ ID NO: 4), forward primer(TGTGTGCCACCAGCAGAGA; SEQ ID NO: 5), and reverse primer(AGTCGAGTCCCATCACCAAAA; SEQ ID NO: 6) were synthesized. cDNA from Day 0SCL-42 PBMCs was prepared as described and was amplified by one round ofPCR using Vβ24-family specific PCR primers (Biomed Immunotech, TampaFla.). Expression of the specific Vβ24 TCRs was determined in triplicateusing standard ABI chemistry and reagents.

EXAMPLE 4

Clinical Descriptions of Anti-RPC1 Positive Patients

As detailed below, the anti-PRC1 positive scleroderma patients withcancer shared many features, including a short interval between thefirst clinical signs of scleroderma and cancer diagnosis, aggressivecutaneous disease, and a high risk of scleroderma renal crisis.

Patient SCL-1

Patient 1 palpated a breast mass in the summer of 2005 and was diagnosedwith a breast invasive ductal carcinoma on Jul. 26, 2005. Around thetime of her diagnosis, she developed hypertension, thrombocytopenia,seizures, and renal failure that progressed despite blood pressurecontrol. She ultimately initiated peritoneal dialysis. Her breast cancerwas treated with lumpectomy, radiation therapy, and doxorubicin. InOctober of 2005, she began to notice Raynaud' s phenomenon, and inOctober of 2007, she developed skin thickening. When first seen in ourCenter on Feb. 4, 2008, she was noted to have extensive and severescleroderma skin thickening with a modified Rodnan skin score (mRSS) of41 (range is 0-51 with 51 representing most severe disease possible).

Patient SCL-2

Patient 2 was noted to have a mass on a chest radiograph, leading to adiagnosis of a small cell carcinoma of the lung on Mar. 22, 2006. Sheclearly had Raynaud' s phenomenon by April 2006. She was treated withchemotherapy (completed July 2006) and radiation therapy withprophylactic brain irradiation (completed September 2006). By April of2007, she began to notice worsening of her Raynaud's phenomenon andswelling of her hands followed by the onset of rapid, diffuse skinthickening. She was initially treated for her cutaneous disease withmycophenolate mofetil and was noted to have a mRSS of 47 on her visit toour Center on Sep. 6, 2007. She later required therapy withcyclophosphamide due to concern for interstitial lung disease, and byDec. 13, 2011, her mRSS had decreased significantly to 5.

Patient SCL-4

Patient 4 had a known BRCA1 mutation and underwent a prophylacticoophorectomy based on her genetic risk. During this procedure, she wasfound to have stage III ovarian adenocarcinoma with papillary serousfeatures (Apr. 5, 2006). She completed 6 cycles of paclitaxel andcisplatin in August 2006, and around this time developed Raynaud'sphenomenon. Her chemotherapy course was complicated by the developmentof pericarditis with tamponade physiology requiring drainage and apericardial window, and there was no evidence of an infected ormalignant effusion. When first seen here on Jan. 10, 2008, she was notedto have significant skin disease (mRSS 21), numerous tendon frictionrubs, a myopathy, and scleroderma renal crisis with a Cr of 1.9. In2008-2009, she was treated with a number of immunosuppressive agentstargeting her cutaneous, muscle, and joint disease includingmycophenolate, methotrexate, azathioprine and hydroxychloroquine, andher skin disease was significantly improved by August 8. In October2011, she developed a small bowel obstruction with imaging findingsconsistent with serosal implants in the context of a rising CA 125level. She began weekly carboplatin, and her CA 125 level had normalizedby April 2012.

Patient SCL-13

Patient 13 noticed bilateral hand and ankle swelling in May 2005 andRaynaud's phenomenon in August 2005. She was diagnosed with invasiveductal carcinoma of the breast on Aug. 24, 2005. She was treated with amastectomy followed by doxorubicin and cyclophosphamide fromOctober-December 2005. In January 2006, she developed worsening skinthickening in her hands, arthralgias and myalgias and began therapy withd-penicillamine and later methotrexate. She also initiated paclitaxeland trastuzumab for her cancer in January 2006. She was seen at ourCenter Apr. 16, 2007 and was noted to have progressive skin disease(mRSS 30); she was transitioned to mycophenolate for her cutaneousdisease and gradually had an improvement in her skin disease (mRSS in2012 was 2).

Patient SCL-35

Patient 35 was diagnosed with breast ductal carcinoma in situ on Aug.16, 2004, treated with a mastectomy. In April 2006, she developedsymptoms consistent with carpal tunnel syndrome, and by August 2006, shehad lower extremity skin thickening and tendon friction rubs. Raynaud'sphenomenon developed in January 2007. When first seen at our Center inJune 2007, her mRSS was 48, and she was on letrozole for her malignancy.After therapy with cyclophosphamide and mycophenolate, her cutaneousdisease significantly improved (mRSS 3 by March 2011).

Patient SCL-42

Patient 42 developed arthralgias and skin thickening in her fingers inMarch 2007 that rapidly progressed to diffuse skin thickening. In April2007 she developed Raynaud's phenomenon also. By October 2007, shedeveloped hypertension requiring ACE-inhibitor therapy, and her mRSS was18. Despite therapy with mycophenolate, her cutaneous diseaseprogressed, and by March 2008, her mRSS had increased to 37. In April2008, methotrexate was added to her regimen with some improvement inflexibility and new hair growth; however her mRSS remained at 35 in July2008. In September 2008, in the setting of increased cutaneous activity,she was diagnosed with a stage II, triple negative, invasive ductalcancer of the breast. She was treated with mastectomy (October 2008) andchemotherapy with cyclophosphamide and docetaxel (December 2008-February2009). Her cutaneous symptoms gradually improved in the setting of IVIGtherapy, and by December 2011 her mRSS was 8.

Patient SCL-81

Patient 81 was diagnosed with an adenocarcinoma of the colon withpositive lymph nodes in May 2005 requiring bowel resection and 5-FU andplatinum chemotherapy. In July 2009, he developed diffuse cutaneous skindisease and by November 2009 had Raynaud's phenomenon. In March 2010,his mRSS was 46.

Patient SCL-82

Patient 82 developed Raynaud's phenomenon and hand swelling in January2008 and was noted to have a mRSS of 14 in August 2008 while onmethotrexate therapy. By January 2009, the patient was on combinationmycophenolate and methotrexate therapy for a mRSS of 18. By January2010, her skin disease was significant improved (mRSS 5), but she wasdiagnosed with a ductal carcinoma in situ (DCIS) of the breast on Jun.28, 2010 and treated with a mastectomy.

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The disclosure of each reference cited is expressly incorporated herein.

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What is claimed is:
 1. A method, comprising: administering to a patienthaving a cancer a peptide of 10-40 contiguous amino acid residues of ahuman, autoimmune antigen, wherein the peptide binds with high affinityto an HLA protein of the patient, wherein the peptide comprises avariant residue relative to the wild-type antigen.
 2. The method ofclaim 1 wherein prior to the step of administering the patient sample istested to ascertain the patient's HLA type.
 3. The method of claim 1wherein the antigen is TOP1.
 4. The method of claim 1 wherein theantigen is CENPB.
 5. The method of claim 1 wherein the antigen is Mi-2.6. The method of claim 1 wherein a full-length version of the antigen isco-administered with the peptide.
 7. The method of claim 1 wherein afull-length, wild-type version of the antigen is co-administered withthe peptide.
 8. The method of claim 1 wherein a full-length, mutantversion of the antigen is co-administered with the peptide, wherein theantigen and the peptide comprise the variant residue.
 9. The method ofclaim 1 wherein the cancer is selected from the group consisting ofbreast, lung, ovarian, colorectal, and B cell lymphoma.
 10. The methodof claim 1 wherein the peptide comprises 10-30 contiguous residues ofthe antigen.
 11. The method of claim 1 wherein the peptide comprises10-20 contiguous residues of the antigen.
 12. The method of claim 1wherein the peptide comprises 13-18 contiguous residues of the antigen.13. The method of claim 1 wherein the antigen is selected from the groupconsisting of CENP A, CENP B, CENP C, topoisomerase-1, nucleophosmin,fibrillarin, UBF, RPP30, RPP40, RPB1, RPB2, P80 coilin, UBF, nucleolin,CEP250, PCM1, TRIM21, components of the exosome complex, PARP1, HistoneH1, Histone H2, Histone H3, Histone H4, SmB, SmD, SmG, U1-70k, Ro52,Ro60, La, Ribosomal P2, Ribosomal P0, Ribosomal P1, Ki-67, PCNA,Defensin beta, Defensin a-4, Defensin a-3, Defensin a-1, LL37, ASF/SF2,SR proteins, IFI-16, AQP4, M3R, Fodrin alpha, Golgin-160, GM130, NuMA,Giantin, RBBP7, CHD4, RBBP4 (NuRD), MBD3, SWI/SNF-related, CHD3, HDAC1,PMS1, PMS2, DNA-PK, RNA helicase DHX15, XRCC4, TIF-1g/TRIM 24, TIF-1b,Ku-70, Ku-86, NXP2/MORC3, HMGCR, PUF-60, FUBP1, PM SCL 100k, PM SCL 40k,Histidyl tRNA synthetase, Alanyl tRNA synthetase, Lysyl tRNA synthetase,Threonyl tRNA synthetase, Asparaginyl tRNA synthetase, MDA5, SRP54, SRP72, SRP19, PALLD, SAE1, SAE2, Pr3, MPO, LAMP2, Vimentin, and PAD4. 14.An isolated peptide of 10-40 contiguous amino acid residues of a human,autoimmune antigen, wherein the peptide binds with high affinity to ahuman HLA protein, wherein the peptide comprises a variant residuerelative to the wild-type antigen.
 15. The isolated peptide of claim 14wherein the antigen is selected from the group consisting of CENP A,CENP B, CENP C, topoisomerase-1, nucleophosmin, fibrillarin, UBF, RPP30,RPP40, RPB1, RPB2, P80 coilin, UBF, nucleolin, CEP250, PCM1, TRIM21,components of the exosome complex, PARP1, Histone H1, Histone H2,Histone H3, Histone H4, SmB, SmD, SmG, U1-70k, Ro52, Ro60, La, RibosomalP2, Ribosomal P0, Ribosomal P1, Ki-67, PCNA, Defensin beta, Defensina-4, Defensin a-3, Defensin a-1, LL37, ASF/SF2, SR proteins, IFI-16,AQP4, M3R, Fodrin alpha, Golgin-160, GM130, NuMA, Giantin, RBBP7, CHD4,RBBP4 (NuRD), MBD3, SWI/SNF-related, CHD3, HDAC1, PMS1, PMS2, DNA-PK,RNA helicase DHX15, XRCC4, TIF-lg/TRIM 24, TIF-1b, Ku-70, Ku-86,NXP2/MORC3, HMGCR, PUF-60, FUBP1, PM SCL 100k, PM SCL 40k, Histidyl tRNAsynthetase, Alanyl tRNA synthetase, Lysyl tRNA synthetase, Threonyl tRNAsynthetase, Asparaginyl tRNA synthetase, MDA5, SRP54, SRP 72, SRP19,PALLD, SAE1, SAE2, Pr3, MPO, LAMP2, Vimentin, and PAD4.
 16. The isolatedpeptide of claim 14 wherein the peptide comprises 10-30 contiguousresidues of the antigen.
 17. The isolated peptide of claim 14 whereinthe peptide comprises 10-20 contiguous residues of the antigen.
 18. Theisolated peptide of claim 14 wherein the peptide comprises 13-18contiguous residues of the antigen.
 19. The isolated peptide of claim 14which is in admixture with a full-length version of the antigen.
 20. Theisolated peptide of claim 19 wherein the full-length version of theantigen is a wild-type antigen.